HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail
ABSTRACT In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organ...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2017-12-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mBio.01272-17 |
| _version_ | 1819038511034007552 |
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| author | Joanna Hołówka Damian Trojanowski Katarzyna Ginda Bartosz Wojtaś Bartłomiej Gielniewski Dagmara Jakimowicz Jolanta Zakrzewska-Czerwińska |
| author_facet | Joanna Hołówka Damian Trojanowski Katarzyna Ginda Bartosz Wojtaś Bartłomiej Gielniewski Dagmara Jakimowicz Jolanta Zakrzewska-Czerwińska |
| author_sort | Joanna Hołówka |
| collection | DOAJ |
| description | ABSTRACT In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones. In this study, we analyzed the in vivo binding of HupB on the chromosome scale. By using PALM (photoactivated localization microscopy) and ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing), we observed that the C-terminal domain is indispensable for the association of HupB with the nucleoid. Strikingly, the in vivo binding of HupB displayed a bias from the origin (oriC) to the terminus (ter) of the mycobacterial chromosome (numbers of binding sites decreased toward ter). We hypothesized that this binding mode reflects a role for HupB in organizing newly replicated oriC regions. Thus, HupB may be involved in coordinating replication with chromosome segregation. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development. |
| first_indexed | 2024-12-21T08:38:28Z |
| format | Article |
| id | doaj.art-3c89f1c0785342979323dd7115daa83f |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-12-21T08:38:28Z |
| publishDate | 2017-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-3c89f1c0785342979323dd7115daa83f2022-12-21T19:10:01ZengAmerican Society for MicrobiologymBio2150-75112017-12-018610.1128/mBio.01272-17HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like TailJoanna Hołówka0Damian Trojanowski1Katarzyna Ginda2Bartosz Wojtaś3Bartłomiej Gielniewski4Dagmara Jakimowicz5Jolanta Zakrzewska-Czerwińska6Laboratory of Molecular Biology of Microorganisms, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, PolandDepartment of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, PolandDepartment of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, PolandLaboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandLaboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandLaboratory of Molecular Biology of Microorganisms, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, PolandLaboratory of Molecular Biology of Microorganisms, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, PolandABSTRACT In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones. In this study, we analyzed the in vivo binding of HupB on the chromosome scale. By using PALM (photoactivated localization microscopy) and ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing), we observed that the C-terminal domain is indispensable for the association of HupB with the nucleoid. Strikingly, the in vivo binding of HupB displayed a bias from the origin (oriC) to the terminus (ter) of the mycobacterial chromosome (numbers of binding sites decreased toward ter). We hypothesized that this binding mode reflects a role for HupB in organizing newly replicated oriC regions. Thus, HupB may be involved in coordinating replication with chromosome segregation. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development.https://journals.asm.org/doi/10.1128/mBio.01272-17HUHupBMycobacteriumchromosome dynamicschromosome organizationnucleoid-associated proteins |
| spellingShingle | Joanna Hołówka Damian Trojanowski Katarzyna Ginda Bartosz Wojtaś Bartłomiej Gielniewski Dagmara Jakimowicz Jolanta Zakrzewska-Czerwińska HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail mBio HU HupB Mycobacterium chromosome dynamics chromosome organization nucleoid-associated proteins |
| title | HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail |
| title_full | HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail |
| title_fullStr | HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail |
| title_full_unstemmed | HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail |
| title_short | HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail |
| title_sort | hupb is a bacterial nucleoid associated protein with an indispensable eukaryotic like tail |
| topic | HU HupB Mycobacterium chromosome dynamics chromosome organization nucleoid-associated proteins |
| url | https://journals.asm.org/doi/10.1128/mBio.01272-17 |
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