1
|
Qin S, Wu H, Li C, Yang J, Yan W, He Z, Xing X, Zhang J, Xu X, Zhao L, Su X. Detection of Naturally occurring abortive transcripts by Base-Stacking Hybridization Assisted Ligation and PCR amplification. Biosens Bioelectron 2024; 251:116099. [PMID: 38330773 DOI: 10.1016/j.bios.2024.116099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Abortive transcripts (ATs) refer to nascent 2-10 nucleotides (nt) RNAs released by RNA polymerases before synthesizing productive RNAs. The quantitative detection of ATs is important for studying transcription initiation and the biological function of ATs; however, no method is available for the qualitative and quantitative assessment of such ultra-short oligonucleotides (typically shorter than 11 nt) in vivo at present, even with the LNA probes, the detection limit can only reach 11 nt. Here, we demonstrated the base stacking hybridization assisted ligation (BSHAL) technique, combined with TaqMan-MGB qPCR, can detect 4-10 nt ATs with a specificity of nucleotide resolution and a sensitivity of approximately 10 pM. By this technique, we detected endogenous ATs in cell lines, mice plasmas, and mice liver tissues, respectively, and proved that naturally occurring ATs do exist. We found that the 8 nt ATs of HMSB and Gapdh could be used as reference ATs for data normalization in Homo and mouse respectively, and 8 nt ATs of Afp and Gpc3 were suitable for use as plasma biomarkers of Hepatocellular carcinoma in mouse, indicate ATs are promising biomarkers. This study offers opportunities to study ATs and other ultra-short oligonucleotides in biological samples.
Collapse
Affiliation(s)
- Shaowei Qin
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Haizhu Wu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Cailin Li
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Jiarui Yang
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, 21218, USA
| | - Weiwei Yan
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Zhigui He
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Xuekun Xing
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Jiayang Zhang
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Xianglin Xu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Lifeng Zhao
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
2
|
Smith EL, Goley ED. House of CarDs: Functional insights into the transcriptional regulator CdnL. Mol Microbiol 2024. [PMID: 38664995 DOI: 10.1111/mmi.15268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/12/2024] [Accepted: 04/11/2024] [Indexed: 07/07/2024]
Abstract
Regulation of bacterial transcription is a complex and multi-faceted phenomenon that is critical for growth and adaptation. Proteins in the CarD_CdnL_TRCF family are widespread, often essential, regulators of transcription of genes required for growth and metabolic homeostasis. Research in the last decade has described the mechanistic and structural bases of CarD-CdnL-mediated regulation of transcription initiation. More recently, studies in a range of bacteria have begun to elucidate the physiological roles of CarD-CdnL proteins as well as mechanisms by which these proteins, themselves, are regulated. A theme has emerged wherein regulation of CarD-CdnL proteins is central to bacterial adaptation to stress and/or changing environmental conditions.
Collapse
Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
3
|
Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. PNAS NEXUS 2024; 3:pgae154. [PMID: 38650860 PMCID: PMC11034885 DOI: 10.1093/pnasnexus/pgae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
Collapse
Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
4
|
Hall AN, Hall BW, Kinney KJ, Olsen GG, Banta AB, Noguera DR, Donohue TJ, Peters JM. Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554875. [PMID: 37662258 PMCID: PMC10473679 DOI: 10.1101/2023.08.25.554875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts have the potential to form the backbone of the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans, Rhodobacter sphaeroides, and Zymomonas mobilis, show particular promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis, N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides. We screen a synthetic promoter library to identify inducible promoters with strong, regulated activity in both organisms. Combining Tn7 integration with promoters from our library, we establish CRISPR interference systems for N. aromaticivorans and R. sphaeroides that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these industrially important species and other Alphaproteobacteria.
Collapse
Affiliation(s)
- Ashley N. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin W. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kyle J. Kinney
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabby G. Olsen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
5
|
Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. J Biol Chem 2023; 299:104724. [PMID: 37075846 PMCID: PMC10232725 DOI: 10.1016/j.jbc.2023.104724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
Bacterial pathogens like Mycobacterium tuberculosis (Mtb) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb. Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase to stabilize the open complex intermediate (RPo) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo. However, it is unknown how CarD achieves promoter-specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RPo stability and test this model using in vitro transcription from a panel of promoters with varying levels of RPo stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnAP3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RPo stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RPo. DNA supercoiling also influenced RPo stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNA polymerase-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
Collapse
Affiliation(s)
- Dennis X Zhu
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA.
| |
Collapse
|
6
|
Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533025. [PMID: 36993566 PMCID: PMC10055060 DOI: 10.1101/2023.03.16.533025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Bacterial pathogens like Mycobacterium tuberculosis ( Mtb ) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb . Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase (RNAP) to stabilize the open complex intermediate (RP o ) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo . However, it is unknown how CarD achieves promoter specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RP o stability and test this model using in vitro transcription from a panel of promoters with varying levels of RP o stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnA P3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RP o stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RP o . DNA supercoiling also influenced RP o stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNAP-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
Collapse
|
7
|
Li X, Chen F, Liu X, Xiao J, Andongma BT, Tang Q, Cao X, Chou SH, Galperin MY, He J. Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response. eLife 2022; 11:73347. [PMID: 35080493 PMCID: PMC8820732 DOI: 10.7554/elife.73347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 12/02/2022] Open
Abstract
Under starvation conditions, bacteria tend to slow down their translation rate by reducing rRNA synthesis, but the way they accomplish that may vary in different bacteria. In Mycobacterium species, transcription of rRNA is activated by the RNA polymerase (RNAP) accessory transcription factor CarD, which interacts directly with RNAP to stabilize the RNAP-promoter open complex formed on rRNA genes. The functions of CarD have been extensively studied, but the mechanisms that control its expression remain obscure. Here, we report that the level of CarD was tightly regulated when mycobacterial cells switched from nutrient-rich to nutrient-deprived conditions. At the translational level, an antisense RNA of carD (AscarD) was induced in a SigF-dependent manner to bind with carD mRNA and inhibit CarD translation, while at the post-translational level, the residual intracellular CarD was quickly degraded by the Clp protease. AscarD thus worked synergistically with Clp protease to decrease the CarD level to help mycobacterial cells cope with the nutritional stress. Altogether, our work elucidates the regulation mode of CarD and delineates a new mechanism for the mycobacterial starvation response, which is important for the adaptation and persistence of mycobacterial pathogens in the host environment.
Collapse
Affiliation(s)
- Xinfeng Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fang Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyu Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfeng Xiao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binda T Andongma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jin He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|