Institut für Molekulare Infektionsbiologie
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The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables “dual RNA-seq” studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
FinO domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts, including mRNAs from many virulence regions, but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis, and virulence genes which is accompanied by altered MAPK (mitogen-activated protein kinase) signaling in the host. Comparison with the other major RNA chaperone in Salmonella, Hfq, reinforces the notion that these two global RNA-binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs (sRNAs), we show that the 3′UTR-derived sRNA STnc540 is capable of repressing an infection-induced magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella pathogenesis and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
IMPORTANCE
The protein ProQ has recently been discovered as the centerpiece of a previously overlooked “third domain” of small RNA-mediated control of gene expression in bacteria. As in vitro work continues to reveal molecular mechanisms, it is also important to understand how ProQ affects the life cycle of bacterial pathogens as these pathogens infect eukaryotic cells. Here, we have determined how ProQ shapes Salmonella virulence and how the activities of this RNA-binding protein compare with those of Hfq, another central protein in RNA-based gene regulation in this and other bacteria. To this end, we apply global transcriptomics of pathogen and host cells during infection. In doing so, we reveal ProQ-dependent transcript changes in key virulence and host immune pathways. Moreover, we differentiate the roles of ProQ from those of Hfq during infection, for both coding and noncoding transcripts, and provide an important resource for those interested in ProQ-dependent small RNAs in enteric bacteria.
Motivation:
Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predi cting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.
Results:
We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.
Cutaneous leishmaniasis is initiated by the bite of an infected sandfly and inoculation of Leishmania major parasites into the mammalian skin. Macrophages are known to playa central role in the course of infection because they are the prime host cells and funetion as antigen-presenting eells (APC) for induetion of the eell-mediated immune response. However, in addition to maerophages in the dermis. the skin eontains epidermal Langerhans eells (LC) which ean present antigen (Ag) to T cells. Therefore, using a murine model of cutaneous leishmaniasis, we analyzed the ability of epidermal cells to induce a T eell response to L.major. The results demonstrated that freshly isolated LC, but not cuItured LC, are highly active in presenting L.major Ag in vitro to T cells from primed mice and to a L.major-specific T cell clone. Furthermore, freshly isolated LC had the ability to retain L.major Ag in immunogenic form for at least 2 days. Their efficiency was much greater than that of irradiated spleen cells, a standard population of APC. LC stimulated both T cell proliferation and production of the Iymphokines interleukin (IL)-2 and IL-4. The response was Ag specific and could be induced by lysate of L. major parasites and by live organisms. The data suggest that epidermal LC are important APC in eutaneous leishmaniasis. They may perform a critical funetion by eapturing L.major Ag in the skin and presenting it either to quiescent T eells circulating through the draining lymph node or locally to T effector cells infiltrating the cutaneous lesion.
Agrobacterium species are capable of interkingdom gene transfer between bacteria and plants. The genome of Agrobacterium tumefaciens consists of a circular and a linear chromosome, the At-plasmid and the Ti-plasmid, which harbors bacterial virulence genes required for tumor formation in plants. Little is known about promoter sequences and the small RNA (sRNA) repertoire of this and other α-proteobacteria. We used a differential RNA sequencing (dRNA-seq) approach to map transcriptional start sites of 388 annotated genes and operons. In addition, a total number of 228 sRNAs was revealed from all four Agrobacterium replicons. Twenty-two of these were confirmed by independent RNA gel blot analysis and several sRNAs were differentially expressed in response to growth media, growth phase, temperature or pH. One sRNA from the Ti-plasmid was massively induced under virulence conditions. The presence of 76 cis-antisense sRNAs, two of them on the reverse strand of virulence genes, suggests considerable antisense transcription in Agrobacterium. The information gained from this study provides a valuable reservoir for an in-depth understanding of sRNA-mediated regulation of the complex physiology and infection process of Agrobacterium.
Saposin-ähnliche Proteine (SAPLIPs) sind membraninteragierende Proteine, die sich durch die konservierte Position von drei Disulfidbrücken, einer typischen alpha-helikalen Proteinfaltung und der Fähigkeit mit Lipiden zu interagieren, auszeichnen. Ihre zellulären Funktionen sind äußerst vielfältig. Bis zum Beginn des Genomsequenzierungsprojektes waren die Amoebapores die einzigen bekannten und charakterisierten SAPLIPs von Entamoeba histolytica, dem Erreger der humanen Amöbenruhr. Aufgrund ihrer antimikrobiellen Aktivität stellen sie für diesen parasitischen Einzeller, der sich von phagozytierten Bakterien ernährt, wichtige Effektormoleküle dar. Sie können aber auch cytolytisch auf Wirtszellen wirken und werden deshalb als bedeutender Pathogenitätsfaktor angesehen. Die theoretische computergestützte Datenbankanalyse nach Abschluss der Genomsequenzierung ergab, dass es 16 weitere Gene kodierend für SAPLIPs zusätzlich zu den drei Amoebapore-Genen gibt. Die Sequenzen der neuen SAPLIPs sind abgesehen von dem Cysteinmotiv divers und auch die Größe der Proteine ist sehr unterschiedlich (77 - 1009 Aminosäuren). Alle besitzen sie jedoch eine einzige, C-terminal gelegene SAPLIP Domäne. Außer der SAPLIP-Domäne konnten keine weiteren bekannten funktionellen oder strukturellen Domänen in den relevanten Datenbanken identifiziert werden, die auf mögliche Funktionen hätten hinweisen können. Alle SAPLIP-Gene werden gleichzeitig in axenisch kultivierten Trophozoiten transkribiert wie durch reverse Transkriptions-PCR gezeigt wurde. Die vergleichende transkriptionelle Analyse im Mikroarray ergab, dass nach Kontakt mit menschlichen Kolonzellen keine Hochregulierung dieser Gene mit Ausnahme des Amoebapore A Gens stattfindet. Für die parallele Klonierung der verschiedenen SAPLIP-Domänen wurde ein ”Expressionsscreening” in E.coli mit dem grün fluoreszierenden Protein als Reporterprotein etabliert, das die erfolgreiche Klonierung und Expression eines Fragments aufgrund der Fluoreszenz der Bakterienkolonie bereits auf der Ebene der Transformation anzeigt. Die rekombinant exprimierte und bis zur Homogenität gereinigte SAPLIP-Domäne von SAPLIP 12 wies Amoebapore-ähnliche Aktivitäten auf. Unter Verwendung von Liposomen konnte porenbildende Aktivität nachgewiesen werden, wobei diese Aktivität stark an einen sauren pH-Wert gebunden ist. Die SAPLIP-Domäne 12 ist aber auch antibakteriell und dieses sogar mit vergleichbarer Selektivität wie Amoebapore A, nämlich Zelllyse von gram-positiven B. megaterium war nachweisbar, jedoch nicht von gram-negativen E. coli. Strukturell unterscheiden sich die SAPLIP-Domäne 12 und Amoebapore A bezüglich der Exposition positiver Ladungsansammlungen auf der Proteinoberfläche und des Fehlens des für den Mechanismus der Amoebapores essentiellen Histidinrestes an entsprechender Position in der Sequenz. Darüber hinaus übt die SAPLIP-Domäne 12 eine im Vergleich zum Amoebapore A geringere spezifische Aktivität aus. Diese Eigenschaften weisen darauf hin, dass es sich um einen anderen Wirkungsmechanismus handeln könnte. Für die SAPLIP-Domäne 12 wäre eine über die positiven Ladungen der Proteinoberfläche vermittelte Interaktion mit den negativ geladenen Phospholipidköpfen von Membranen denkbar, die bei Erreichen einer bestimmten Konzentration in einer Störung der Lipidordnung und letztendlich in der Auflösung der Membranstruktur resultieren könnte. SAPLIP 3 ähnelt den Amoebapores in der Größe und molekularen Architektur und kann somit als funktionelle Einheit angesehen werden, es unterscheidet sich aber durch eine hohe negative Nettoladung von den Amoebapores. Außerdem ist das rekombinante SAPLIP 3 nicht antibakteriell und die Membraninteraktionen dieses SAPLIPs unterscheiden sich grundlegend von denjenigen, die für die Amoebapores beschrieben sind. SAPLIP 3 zerstört nicht einfach die Liposomenstruktur wie von den porenbildenden Amoebapores bekannt, sondern es vermittelt die Fusion von multilamellaren Liposomen unter Freisetzung des Liposomeninhalts. Diese Aktivität ist abhängig von der Anwesenheit anionischer Lipide und von einem sauren pH-Wert. Die Fähigkeit zur Vesikelfusion sowie die Verteilung der negativen Ladungen von SAPLIP 3 auf der Proteinoberfläche ähneln Merkmalen des humanen Saposin C. Neben der Funktion als Cofaktor von Exohydrolasen, die im Sphingolipid Katabolismus involviert sind, wird angenommen, dass die Fähigkeit von Saposin C, Vesikel zu fusionieren, wichtig für die Reorganisation der humanen lysosomalen Kompartimente ist. Die Saposin C-ähnlichen Charakteristika von SAPLIP 3 geben Grund zu der Annahme, dass es bereits in einem so basalen Organismus wie der Amöbe ein Protein mit Saposin-ähnlichen membranfusionierenden Aktivitäten gibt und dass dieses SAPLIP entsprechende Funktionen während endo- und exozytotischer Transportprozesse in der Amöbe übernehmen könnte.
Die MHK-Werte von Desacetylcefotaxim gegen verschiedene, z. T. ampicillinresistente Stämme von Escherichia coH, die mit Hilfe einer Agardilutionsmethode erhoben wurden, waren höher als die von Cefotaxim und Ceftriaxon, jedoch niedriger als die von Cefoxitin. In einem Modell der systemischen Infektion der Maus mit einem plasmidtragenden, betalactamaseproduzierenden Stamm von E. coli führte die Therapie mit Desacetylcefotaxim zu einer starken Reduktion der Keime pro Leber. Im Vergleich zur Therapie mit Cefotaxim trat die protektive Wirkung aber verlangsamt ein. Desacetylcefotaxim ist also kein unnützes Abbauprodukt von Cefotaxim.
The massive remodeling of the heart tissue, as observed in response to pressure overload or myocardial infarction, is considered to play a causative role in the development of heart failure. Alterations in the heart architecture clearly affect the mechanical properties of the heart muscle, but they are rooted in changes at the cellular level including modulation of gene expression. Together with integrins, the transmembrane receptors linking the extracellular environment to the cytoskeleton, extracellular matrix (ECM) proteins and matricellular proteins are key components of the remodeling process in the heart. Therefore, this thesis was aimed at analysing the role of integrins in the regulation of gene expression and heart muscle performance during cardiac wound repair induced by pressure overload or myocardial infarction (MI). To investigate the contribution of integrin Beta 1, we characterised the response of mice with a conditional, cardiac-specific deletion of the integrin Beta 1 gene in an experimental model of pressure overload by aortic banding (AB). In particular, we measured physiological alterations and gene expression events in the stressed heart in the presence or absence of integrin Beta 1. Interestingly, mice containing a knock-out allele and the ventricular myocyte-specific conditional allele of the integrin Beta 1 gene were born and grew up to adulthood. Though these animals still exhibited minor amounts of integrin Beta1 in the heart (expressed by non-myocytes), these mice displayed abnormal cardiac function and were highly sensitive to AB. Whereas a compensatory hypertrophic response to pressure overload was observed in wildtype mice, the integrin Beta 1-deficient mice were not able to undergo heart tissue remodeling. Furthermore, ECM gene expression was altered and, in particular, the increased expression of the matricellular protein SPARC after AB was abolished in integrin Beta 1–deficient mice. Interestingly, we also found a transient upregulation of SPARC mRNA during heart remodeling after MI using cDNA macroarrays. Indeed, increased SPARC protein levels were observed starting at day 2 (2.55±0.21fold, p<0.01), day 7 (3.72±0.28 fold, p<0.01) and 1 month (1.9±0.16 fold, p<0.01) after MI, which could be abolished by using an integrin alpha v inhibitor in vivo. Immunofluorescence analysis of heart tissue demonstrated that the increased SPARC expression was confined to the infarcted area and occurred together with the influx of fibroblasts into the heart. In vitro, either TGF-Beta 1 or PDGF-BB stimulated SPARC expression by fibroblasts. Inhibition of integrin alpha v did not interfere with TGF-Beta1 or PDGF induced SPARC secretion as determined by ELISA assays or Western blot. However, secretion of TGF-Beta1 and PDGF-BB by cardiomyocytes was induced by vitronectin, a ligand of integrin alpha v, and this response was blocked by the integrin alpga v inhibitor. Functionally, SPARC modulated the migratory response of fibroblasts towards ECM proteins suggesting that the local deposition of SPARC following MI contributes to scar formation. Taken together, our combined in vivo and in vitro data demonstrate that several integrin subunits play critical roles during tissue remodeling in the injured heart. Integrin-dependent gene expression events such as the upregulation of SPARC following MI are critical to orchestrate the healing response. These processes appear to involve complex cross-talk between different cell types such as cardiomyocytes and fibroblasts to allow for locally confined scar formation. The elucidation of the sophisticated interplay between integrins, matricellular proteins such as SPARC, and growth factors will undoubtedly provide us with a better and clinically useful understanding of the molecular mechanisms governing heart remodeling.
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain’s evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.
Asymptomatische Bakteriurie (ABU) stellt eine bakterielle Infektion der Harnblase über einen langen Zeitraum dar, die häufig von Escherichia coli hervorgerufen wird, ohne dass typische Symptome einer Harnwegsinfektion auftreten. Um die Charakteristika von ABU E. coli Isolaten genauer zu untersuchen, wurden die Geno- und Phänotypen von 11 ABU-Isolaten verglichen. Außerdem wurden in mehreren aufeinanderfolgenden in vivo-Reisolaten des Modell-ABU Stammes 83972 die Veränderungen im Transkriptom, Proteom und Genom während einer langfristigen Persistenz in der menschlichen Blase charakterisiert. Schließlich wurde der Effekt des menschlichen Wirtes auf die bakterielle Adaptation durch einen Vergleich von in vitro- mit in vivo-kultivierten Stämmen abgeschätzt. ABU-Isolate stellt eine heterogene Gruppe von Organismen dar. Diese können den vier phylogenetischen Hauptgruppen von E. coli sowie unterschiedlichen klonalen Gruppen zugeordnet werden. Dementsprechend unterscheiden sie sich erheblich bezüglich der Zusammensetzung des Genomes, der Genomgröße und auch der Ausstattung mit UPEC-typischen Virulenz-assoziierten Genen. Multi-Lokus-Sequenz-Typisierung legt nahe, dass bestimmte ABU Stämme sich durch Genomreduktion aus UPEC Stämmen entwickelt haben, die eine Harnwegsinfektion mit charakteristischen Symptomen auslösen konnten. Folglich erlaubt die hohe Genomplastizität von E. coli keine generalisierte Betrachtung einzelner Isolate eines Klons. Genomreduktion über Punktmutationen, Genom-Reorganisation und Deletionen resultierte in der Inaktivierung einiger Gene, die für einige UPEC Virulenz-Faktoren kodieren. Dies stützt die Vorstellung, dass eine verminderte bakterielle Aktivierung der Entzündung der Wirtsschleimhaut den Lebensstil von ABU (bei diesen E. coli-)Isolaten fördert. Genregulation und genetische Diversität sind Strategien, die es Bakterien ermöglichen unter sich fortlaufend ändernden Bedingungen zu leben bzw. zu überleben. Um die anpassungsbedingten Veränderungen bei einem langfristigen Wachstum in der Blase zu untersuchen, wurden aufeinanderfolgende Reisolate, denen eine langfristige in vivo-Kolonisierung im menschlichen Wirt beziehungsweise eine in vitro-Kultivierung vorausgegangen ist, im Hinblick auf Veränderungen Genexpression und Genomorganisation analysiert. In diesem Zusammenhang konnte gezeigt werden, dass E. coli in der Lage ist, seine metabolischen Netzwerke verschiedenen Wachstumsbedingungen anzupassen und individuelle bakterielle Kolonisierungsstrategien entwickeln kann. Transkriptom- und Proteom-Analysen zeigten verschiedene metabolische Strategien zur Nährstoffbeschaffung und Energieproduktion bei untersuchten in vivo-Reisolaten vom Stamm 83972, die es ihnen ermöglichen, den Wirt zu kolonisieren. Das Zurückgreifen auf D-Serin, Deoxy- und Ribonucleoside sowie die bidirektionale Umwandlung zwischen Pentose und Glucuronat waren hoch-regulierte Stoffwechselwege, die die in vivo-Reisolate mit zusätzlicher Energie für ein effizientes Wachstum in der Blase versorgen. Zudem wurden in dieser Studie die Netzwerke für eine Reaktion auf Abwehrmechanismen des Wirtes erforscht: Erstmals wurde hier die Rolle der Klasse-III-Alkoholdehydrogenase AdhC, bekannt durch ihre Bedeutung bei der Entgiftung von Stickstoffmonoxid, bei der Wirtsantwort während einer asymptomatischen Bakteriurie gezeigt. Aufeinanderfolgende in vivo- und in vitro-Reisolate vom Stamm 83972 wurden ebenfalls bezüglich ihrer Genomstruktur analysiert. Einige Veränderungen in der Genomstruktur der aufeinanderfolgenden Reisolate, die von einer humanen Kolonisierungsstudie stammen, implizieren die Bedeutung einer Interaktion der Bakterien mit dem Wirt bei der Mikroevolution der Bakterien. Dagegen war die Genomstruktur von Reisolaten eines langfristigen in vitro-Kultivierungsexperiments, bei dem sich der Stamm 83972 ohne Wirtskontakt vermehrt hat, nicht von Veränderungen betroffen. Das legt nahe, dass die Immunantwort eine Genomplastizität fördert und somit eine treibende Kraft für den ABU Lebensstil und die Evolution im Harnwegstrakt ist.
Escherichia coli isolates of serotype 06: K5 are the most common causative agents of cystitis and pyelonephritis in adults. To answer the question, as to whether strains of this particular serotype represent one special clonal group, out of a collection of 34 serotype 06: K5 isolates [Zingler et al. ( 1990) Zentralbl. Bakteriol Mikrobiol Hyg [A] 274:372-381] 15 strains were selected andanalyzed in detail. The flagellar (H) antigen and the outer membrane protein (OMP) pattern were determined. Furtherserum resistance properties and the genetic presence and expression of other virulence factors, including hemolysin, aerobactin, P fimbriae, S/F1C fimbriae and type 1 fimbriae was evaluated. In~laddition the Xbalmacrorestriction pattern of ten representative isolates was elaborated and the fimbrial (F) antigentype ofthe P fimbriae was determined, to obtain the complete 0: K: H: F pattern. These analyses could clearly show that the 06: K5 isolates do not represent one clonal group. The Xbal-macrorestriction profiles were heterogeneaus and marked differences in the hybridization patterns, using virulenceassociated gene probes in Southern hybridization of long-range-separated genomic DNA, were observed among the strains. However, some of strains showed similarities in the genomic profiles, arguing for clonal groupings among the 06: K5 isolates. lnterstingly the strains grouped tagether exhibited the same fimbrial F typethat many indicate a coincidence of this phenotypic trait with clonality.
A total of 36 Escherichia coli urinary tract isolates (UTI) of serotype 06, with different combinations of capsule ( K) and flagellin ( H) antigens, were analysed according to the outer membrane pattern (OMP), serum resistance properties, mannose-resistant hemagglutination using various types of erythrocytes, and also for the genetic presence and the expression of Pfimbriae. S fimbriae/F1 C fimbriae, Type 1 fimbriae, aerobactin and hemolysin. Twenty selected strains were further analysed by pulsed field gel electrophoresis (PFGE), elaborating genomic profilas by Xba I cleavage and subsequent Southern hybridization to virulence-associated DNA probes. lt could be shown that 06 UTI isolates represent a highly heterogeneaus group of strains according to the occurrence and combination of these traits. Relatedness an the genetic and the phenotypic Ievei was found for some of the strains exhibiting the same 0: K: H: F serotype. DNA Iang-range mapping further indicated some interesting features, according to the copy number and the genomic linkage of virulence genes.
Microcin C (McC) is a peptide-nucleotide antibiotic produced by Escherichia coli cells harboring a plasmid-borne operon mccABCDE. The heptapeptide MccA is converted into McC by adenylation catalyzed by the MccB enzyme. Since MccA is a substrate for MccB, a mechanism that regulates the MccA/MccB ratio likely exists. Here, we show that transcription from a promoter located upstream of mccA directs the synthesis of two transcripts: a short highly abundant transcript containing the mccA ORF and a longer minor transcript containing mccA and downstream ORFs. The short transcript is generated when RNA polymerase terminates transcription at an intrinsic terminator located in the intergenic region between the mccA and mccB genes. The function of this terminator is strongly attenuated by upstream mcc sequences. Attenuation is relieved and transcription termination is induced when ribosome binds to the mccA ORF. Ribosome binding also makes the mccA RNA exceptionally stable. Together, these two effects-ribosome induced transcription termination and stabilization of the message-account for very high abundance of the mccA transcript that is essential for McC production. The general scheme appears to be evolutionary conserved as ribosome-induced transcription termination also occurs in a homologous operon from Helicobacter pylori.
Background
Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters.
Results
A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file.
Conclusions
The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.