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Chen Y, Lin Y, Zhu J, Zhou J, Lin H, Fu Y, Zhou Y. Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions. Front Microbiol 2024; 15:1323160. [PMID: 38500581 PMCID: PMC10945327 DOI: 10.3389/fmicb.2024.1323160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/12/2024] [Indexed: 03/20/2024] Open
Abstract
The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium Klebsiella aerogenes strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate-free or potassium nitrate-rich media. Overall, K. aerogenes B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between K. aerogenes B23 cultured on potassium nitrate-free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of K. aerogenes B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, FNR, NarK/14945, fdx, gshA, proB, proA, gapA, argH, artQ, artJ, artM, ArgR, GAT1, prmB, pyrG, glnS, and Ca1 were significantly upregulated in the nitrogen-treated K. aerogenes B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, norV, norR, and narI were also upregulated in nitrogen-treated K. aerogenes B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in K. aerogenes B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism-associated genes in K. aerogenes B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how K. aerogenes B23 utilizes nutritional elements.
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Affiliation(s)
| | | | | | | | | | | | - Yan Zhou
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
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Kress-Bennett JM, Hiller NL, Eutsey RA, Powell E, Longwell MJ, Hillman T, Blackwell T, Byers B, Mell JC, Post JC, Hu FZ, Ehrlich GD, Janto BA. Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae. PLoS One 2016; 11:e0149891. [PMID: 26977929 PMCID: PMC4792463 DOI: 10.1371/journal.pone.0149891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 02/05/2016] [Indexed: 12/11/2022] Open
Abstract
Haemophilus influenzae is an opportunistic pathogen. The emergence of virulent, non-typeable strains (NTHi) emphasizes the importance of developing new interventional targets. We screened the NTHi supragenome for genes encoding surface-exposed proteins suggestive of immune evasion, identifying a large family containing Sel1-like repeats (SLRs). Clustering identified ten SLR-containing gene subfamilies, each with various numbers of SLRs per gene. Individual strains also had varying numbers of SLR-containing genes from one or more of the subfamilies. Statistical genetic analyses of gene possession among 210 NTHi strains typed as either disease or carriage found a significant association between possession of the SlrVA subfamily (which we have termed, macrophage survival factor, msf) and the disease isolates. The PittII strain contains four chromosomally contiguous msf genes. Deleting all four of these genes (msfA1-4) (KO) resulted in a highly significant decrease in phagocytosis and survival in macrophages; which was fully complemented by a single copy of the msfA1 gene. Using the chinchilla model of otitis media and invasive disease, the KO strain displayed a significant decrease in fitness compared to the WT in co-infections; and in single infections, the KO lost its ability to invade the brain. The singly complemented strain showed only a partial ability to compete with the WT suggesting gene dosage is important in vivo. The transcriptional profiles of the KO and WT in planktonic growth were compared using the NTHi supragenome array, which revealed highly significant changes in the expression of operons involved in virulence and anaerobiosis. These findings demonstrate that the msfA1-4 genes are virulence factors for phagocytosis, persistence, and trafficking to non-mucosal sites.
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Affiliation(s)
- Jennifer M. Kress-Bennett
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory A. Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Mark J. Longwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Todd Hillman
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Tenisha Blackwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Byers
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Joshua C. Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Fen Z. Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin A. Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Ravcheev DA, Gerasimova AV, Mironov AA, Gelfand MS. Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics 2007; 8:54. [PMID: 17313674 PMCID: PMC1805755 DOI: 10.1186/1471-2164-8-54] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 02/21/2007] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-proteobacteria the composition of global respiration regulators may be different. RESULTS In this study we applied a comparative genomic approach to the analysis of three global regulatory systems, Fnr, ArcA and NarP. These systems were studied in available genomes containing these three regulators, but lacking NarL. So, we considered several representatives of Pasteurellaceae, Vibrionaceae and Yersinia spp. As a result, we identified new regulon members, functioning in respiration, central metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, citrate cicle, metabolism of pyruvate and lactate), metabolism of carbohydrates and fatty acids, transcriptional regulation and transport, in particular: the ATP synthase operon atpIBEFHAGCD, Na+-exporting NADH dehydrogenase operon nqrABCDEF, the D-amino acids dehydrogenase operon dadAX. Using an extension of the comparative technique, we demonstrated taxon-specific changes in regulatory interactions and predicted taxon-specific regulatory cascades. CONCLUSION A comparative genomic technique was applied to the analysis of global regulation of respiration in ten gamma-proteobacterial genomes. Three structurally different but functionally related regulatory systems were described. A correlation between the regulon size and the position of a transcription factor in regulatory cascades was observed: regulators with larger regulons tend to occupy top positions in the cascades. On the other hand, there is no obvious link to differences in the species' lifestyles and metabolic capabilities.
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Affiliation(s)
- Dmitry A Ravcheev
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
| | | | - Andrey A Mironov
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
- State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
| | - Mikhail S Gelfand
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russia
- Institute for Information Transmission Problems, Moscow, 127994, Russia
- State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
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