Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics
The Serratia marcescens is a Gram-negative bacterium from the Enterobacteriaceae family. Recently, S. marcescens have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) acti...
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| creator | Rishen Narayan Dev, Balamurugan Kishan Raj, Selva Raju Chinni, Suresh V. Citartan, Marimuthu |
| description | The
Serratia marcescens
is a Gram-negative bacterium from the
Enterobacteriaceae
family. Recently,
S. marcescens
have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of
S. marcescens
was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from
Salmonella typhi
,
Escherichia coli
, and
Yersinia pestis
against
S. marcescens
was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from
S. typhi
showed expression in
S. marcescens
during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from
S. marcescens
, which can be useful for diagnostics and therapeutic applications. |
| doi_str_mv | 10.1007/s12088-023-01160-y |
| format | Article |
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Serratia marcescens
is a Gram-negative bacterium from the
Enterobacteriaceae
family. Recently,
S. marcescens
have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of
S. marcescens
was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from
Salmonella typhi
,
Escherichia coli
, and
Yersinia pestis
against
S. marcescens
was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from
S. typhi
showed expression in
S. marcescens
during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from
S. marcescens
, which can be useful for diagnostics and therapeutic applications.</description><identifier>ISSN: 0046-8991</identifier><identifier>EISSN: 0973-7715</identifier><identifier>DOI: 10.1007/s12088-023-01160-y</identifier><identifier>PMID: 38468749</identifier><language>eng</language><publisher>New Delhi: Springer India</publisher><subject>Bacteria ; beta-lactamase ; Biomedical and Life Sciences ; death ; Drug resistance ; E coli ; Escherichia coli ; family ; Gene expression ; gene expression regulation ; Gram-negative bacteria ; health services ; Homology ; Life Sciences ; Medical Microbiology ; Microbiology ; Multidrug resistance ; multiple drug resistance ; Opportunist infection ; opportunistic pathogens ; Original Research Article ; Pathogenesis ; Pathogens ; Proteins ; reverse transcriptase polymerase chain reaction ; Reverse transcription ; RNA ; Salmonella Typhi ; Serratia marcescens ; Stationary phase ; Therapeutic applications ; Transcriptomics ; Virulence ; world wide web ; Yersinia pestis ; β Lactamase</subject><ispartof>Indian journal of microbiology, 2024-03, Vol.64 (1), p.198-204</ispartof><rights>Association of Microbiologists of India 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c359t-a7f4ef8874095fc8589e1cf0dd258af3d7a23d7b1a74f7b98017ce967d9fb6a33</cites><orcidid>0000-0003-2874-7440</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12088-023-01160-y$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12088-023-01160-y$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38468749$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rishen Narayan Dev, Balamurugan</creatorcontrib><creatorcontrib>Kishan Raj, Selva Raju</creatorcontrib><creatorcontrib>Chinni, Suresh V.</creatorcontrib><creatorcontrib>Citartan, Marimuthu</creatorcontrib><title>Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics</title><title>Indian journal of microbiology</title><addtitle>Indian J Microbiol</addtitle><addtitle>Indian J Microbiol</addtitle><description>The
Serratia marcescens
is a Gram-negative bacterium from the
Enterobacteriaceae
family. Recently,
S. marcescens
have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of
S. marcescens
was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from
Salmonella typhi
,
Escherichia coli
, and
Yersinia pestis
against
S. marcescens
was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from
S. typhi
showed expression in
S. marcescens
during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from
S. marcescens
, which can be useful for diagnostics and therapeutic applications.</description><subject>Bacteria</subject><subject>beta-lactamase</subject><subject>Biomedical and Life Sciences</subject><subject>death</subject><subject>Drug resistance</subject><subject>E coli</subject><subject>Escherichia coli</subject><subject>family</subject><subject>Gene expression</subject><subject>gene expression regulation</subject><subject>Gram-negative bacteria</subject><subject>health services</subject><subject>Homology</subject><subject>Life Sciences</subject><subject>Medical Microbiology</subject><subject>Microbiology</subject><subject>Multidrug resistance</subject><subject>multiple drug resistance</subject><subject>Opportunist infection</subject><subject>opportunistic pathogens</subject><subject>Original Research Article</subject><subject>Pathogenesis</subject><subject>Pathogens</subject><subject>Proteins</subject><subject>reverse transcriptase polymerase chain reaction</subject><subject>Reverse transcription</subject><subject>RNA</subject><subject>Salmonella Typhi</subject><subject>Serratia marcescens</subject><subject>Stationary phase</subject><subject>Therapeutic applications</subject><subject>Transcriptomics</subject><subject>Virulence</subject><subject>world wide web</subject><subject>Yersinia pestis</subject><subject>β Lactamase</subject><issn>0046-8991</issn><issn>0973-7715</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqFkU1PVDEUhhsiAUT_AAvSxA2bSnv7vSQTERLERHHd9Pa2Q8ncdmjvmIzxx9vxAiYudNM25zznPef0BeCE4PcEY3leSYeVQrijCBMiMNrugSOsJUVSEv6qvTETSGlNDsHrWh8w5kILfgAOqWJCSaaPwM_rwacphujsFHOCNg1wcW-LdZMv8ccczAHe5oTWJU8-JrjIQ0xL-OX2Al7lMa_yssIW_upLabyFn2xxvjqfKuy3jR7Xdpf47uFdsam6EtdTHqOrb8B-sKvq3z7dx-Db5Ye7xRW6-fzxenFxgxzlekJWBuaDagNjzYNTXGlPXMDD0HFlAx2k7drREytZkL1WmEjntZCDDr2wlB6Ds1m3bfC48XUyY2zzrVY2-byphhJOBSYd0f9FO81F-2rKWEPf_YU-5E1JbZEdxZjUVIlGdTPlSq61-GDWJY62bA3BZmejmW00zUbz20azbUWnT9KbfvTDS8mzbw2gM1BbKi19-dP7H7K_AHDLqfU</recordid><startdate>20240301</startdate><enddate>20240301</enddate><creator>Rishen Narayan Dev, Balamurugan</creator><creator>Kishan Raj, Selva Raju</creator><creator>Chinni, Suresh V.</creator><creator>Citartan, Marimuthu</creator><general>Springer India</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0003-2874-7440</orcidid></search><sort><creationdate>20240301</creationdate><title>Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics</title><author>Rishen Narayan Dev, Balamurugan ; Kishan Raj, Selva Raju ; Chinni, Suresh V. ; Citartan, Marimuthu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c359t-a7f4ef8874095fc8589e1cf0dd258af3d7a23d7b1a74f7b98017ce967d9fb6a33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bacteria</topic><topic>beta-lactamase</topic><topic>Biomedical and Life Sciences</topic><topic>death</topic><topic>Drug resistance</topic><topic>E coli</topic><topic>Escherichia coli</topic><topic>family</topic><topic>Gene expression</topic><topic>gene expression regulation</topic><topic>Gram-negative bacteria</topic><topic>health services</topic><topic>Homology</topic><topic>Life Sciences</topic><topic>Medical Microbiology</topic><topic>Microbiology</topic><topic>Multidrug resistance</topic><topic>multiple drug resistance</topic><topic>Opportunist infection</topic><topic>opportunistic pathogens</topic><topic>Original Research Article</topic><topic>Pathogenesis</topic><topic>Pathogens</topic><topic>Proteins</topic><topic>reverse transcriptase polymerase chain reaction</topic><topic>Reverse transcription</topic><topic>RNA</topic><topic>Salmonella Typhi</topic><topic>Serratia marcescens</topic><topic>Stationary phase</topic><topic>Therapeutic applications</topic><topic>Transcriptomics</topic><topic>Virulence</topic><topic>world wide web</topic><topic>Yersinia pestis</topic><topic>β Lactamase</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rishen Narayan Dev, Balamurugan</creatorcontrib><creatorcontrib>Kishan Raj, Selva Raju</creatorcontrib><creatorcontrib>Chinni, Suresh V.</creatorcontrib><creatorcontrib>Citartan, Marimuthu</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Indian journal of microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rishen Narayan Dev, Balamurugan</au><au>Kishan Raj, Selva Raju</au><au>Chinni, Suresh V.</au><au>Citartan, Marimuthu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics</atitle><jtitle>Indian journal of microbiology</jtitle><stitle>Indian J Microbiol</stitle><addtitle>Indian J Microbiol</addtitle><date>2024-03-01</date><risdate>2024</risdate><volume>64</volume><issue>1</issue><spage>198</spage><epage>204</epage><pages>198-204</pages><issn>0046-8991</issn><eissn>0973-7715</eissn><abstract>The
Serratia marcescens
is a Gram-negative bacterium from the
Enterobacteriaceae
family. Recently,
S. marcescens
have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of
S. marcescens
was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from
Salmonella typhi
,
Escherichia coli
, and
Yersinia pestis
against
S. marcescens
was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from
S. typhi
showed expression in
S. marcescens
during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from
S. marcescens
, which can be useful for diagnostics and therapeutic applications.</abstract><cop>New Delhi</cop><pub>Springer India</pub><pmid>38468749</pmid><doi>10.1007/s12088-023-01160-y</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0003-2874-7440</orcidid></addata></record> |
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| subjects | Bacteria beta-lactamase Biomedical and Life Sciences death Drug resistance E coli Escherichia coli family Gene expression gene expression regulation Gram-negative bacteria health services Homology Life Sciences Medical Microbiology Microbiology Multidrug resistance multiple drug resistance Opportunist infection opportunistic pathogens Original Research Article Pathogenesis Pathogens Proteins reverse transcriptase polymerase chain reaction Reverse transcription RNA Salmonella Typhi Serratia marcescens Stationary phase Therapeutic applications Transcriptomics Virulence world wide web Yersinia pestis β Lactamase |
| title | Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics |
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