title: Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA

authors: Petridis, Michael

subjects: Science & Technology

abstract: Soil-dwelling bacteria of the phylum actinomycetes generally harbor either GlnR or AmtR as a global regulator of nitrogen metabolism. Mycobacterium smegmatis harbors both of these canonical regulators; GlnR regulates the expression of key genes involved in nitrogen metabolism, while the function and signal transduction pathway of AmtR in M. smegmatis remains largely unknown. Here, we report the structure and function of the M. smegmatis AmtR and describe the role of AmtR in the regulation of nitrogen metabolism in response to nitrogen availability. To determine the function of AmtR in M. smegmatis, we performed genome-wide expression profiling comparing the wild-type versus an ΔamtR mutant and identified significant changes in the expression of 11 genes, including an operon involved in urea degradation. An AmtR consensus-binding motif (CTGTC-N4-GACAG) was identified in the promoter region of this operon, and ligand-independent, high-affinity AmtR binding was validated by both electrophoretic mobility shift assays and surface plasmon resonance measurements. We confirmed the transcription of a cis-encoded small RNA complementary to the gene encoding AmtR under nitrogen excess, and we propose a post-transcriptional regulatory mechanism for AmtR. The three-dimensional X-ray structure of AmtR at 2.0 Å revealed an overall TetR-like dimeric structure, and the alignment of the M. smegmatis AmtR and Corynebacterium glutamicum AmtR regulatory domains showed poor structural conservation, providing a potential explanation for the lack of M.smegmatisAmtRinteractionwith the adenylylated PII protein. Taken together, our data suggest an AmtR (repressor)/GlnR (activator) competitive binding mechanism for transcriptional regulation of urea metabolism that is controlled by a cis-encoded small antisense RNA.

text: Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA Soil-dwelling bacteria of the phylum actinomycetes generally harbor either GlnR or AmtR as a global regulator of nitrogen metabolism. Mycobacterium smegmatis harbors both of these canonical regulators; GlnR regulates the expression of key genes involved in nitrogen metabolism, while the function and signal transduction pathway of AmtR in M. smegmatis remains largely unknown. Here, we report the structure and function of the M. smegmatis AmtR and describe the role of AmtR in the regulation of nitrogen metabolism in response to nitrogen availability. To determine the function of AmtR in M. smegmatis, we performed genome-wide expression profiling comparing the wild-type versus an ΔamtR mutant and identified significant changes in the expression of 11 genes, including an operon involved in urea degradation. An AmtR consensus-binding motif (CTGTC-N4-GACAG) was identified in the promoter region of this operon, and ligand-independent, high-affinity AmtR binding was validated by both electrophoretic mobility shift assays and surface plasmon resonance measurements. We confirmed the transcription of a cis-encoded small RNA complementary to the gene encoding AmtR under nitrogen excess, and we propose a post-transcriptional regulatory mechanism for AmtR. The three-dimensional X-ray structure of AmtR at 2.0 Å revealed an overall TetR-like dimeric structure, and the alignment of the M. smegmatis AmtR and Corynebacterium glutamicum AmtR regulatory domains showed poor structural conservation, providing a potential explanation for the lack of M.smegmatisAmtRinteractionwith the adenylylated PII protein. Taken together, our data suggest an AmtR (repressor)/GlnR (activator) competitive binding mechanism for transcriptional regulation of urea metabolism that is controlled by a cis-encoded small antisense RNA.

year: 2016-10-23

title: Student perceptions of higher education science and engineering learning communities

authors: Cronje, Tom

subjects: higher education

abstract: This paper presents student perceptions of higher education science and engineering learning communities derived from a cross-case analysis of four case studies across the New Zealand university and polytechnic sectors. Here we explore student expectations and experiences of the higher education sector and canvas their views as to the infrastructure and resources in their institutions of study, and how they see their learning serves their careers' aims. Student perceptions of pedagogies employed in their institutions along with their preferred pedagogies follows, including staff-student interactions and consideration of the importance of practical skill development. The paper finishes by considering student perceptions of support structures and an analysis of their understanding of aspects of the nature of science (NoS) and engineering. The research findings suggest the students feel they become more independent and responsible for their own learning, enjoy smaller class sizes and interactive learning activities such as practical work and tutorials, and they stressed the importance of establishing good relationships with their teachers. Polytechnic students were more positive about their learning and felt the practice features of their learning led to enhanced career prospects. Students from university and polytechnic sectors were aware of formal learning support structures but only used them as a last resort, instead they first worked with peers and teachers.

text: Student perceptions of higher education science and engineering learning communities This paper presents student perceptions of higher education science and engineering learning communities derived from a cross-case analysis of four case studies across the New Zealand university and polytechnic sectors. Here we explore student expectations and experiences of the higher education sector and canvas their views as to the infrastructure and resources in their institutions of study, and how they see their learning serves their careers' aims. Student perceptions of pedagogies employed in their institutions along with their preferred pedagogies follows, including staff-student interactions and consideration of the importance of practical skill development. The paper finishes by considering student perceptions of support structures and an analysis of their understanding of aspects of the nature of science (NoS) and engineering. The research findings suggest the students feel they become more independent and responsible for their own learning, enjoy smaller class sizes and interactive learning activities such as practical work and tutorials, and they stressed the importance of establishing good relationships with their teachers. Polytechnic students were more positive about their learning and felt the practice features of their learning led to enhanced career prospects. Students from university and polytechnic sectors were aware of formal learning support structures but only used them as a last resort, instead they first worked with peers and teachers.

year: 2008

title: Mapping Māori knowledge from the past to inform marine management futures

authors: Paul-Burke, Kura

subjects: mātauranga Māori

abstract: This article provides an overview of research which used mātauranga moana (Māori marine knowledge systems) to inform and assist Western science field research methods and surveys. Place-based Māori marine knowledge identified the traditional distribution range and sizing of taonga (culturally important) species in traditional coastal areas which had been fished and managed by consecutive generations of Māori; kina, Evechinus chloroticus, sea urchin; koura, Jasus edwardsii, red rock lobster; kūtai, Perna canaliculus, green lipped mussel; and pāua, Haliotis iris, abalone. This knowledge was then mapped and used as the baseline for sub-tidal marine science field research surveys. Findings from the transdisciplinary marine research was used to develop management actions to assist Māori and Government entities for improving, enhancing and safeguarding marine taonga species into the future. This article critically discusses and demonstrates the relevance and complementarity of mātauranga Māori and Western science, and the importance of kaupapa Māori strategies for empowering Māori collaboration and voices in marine research co-development, implementation and communication.

text: Mapping Māori knowledge from the past to inform marine management futures This article provides an overview of research which used mātauranga moana (Māori marine knowledge systems) to inform and assist Western science field research methods and surveys. Place-based Māori marine knowledge identified the traditional distribution range and sizing of taonga (culturally important) species in traditional coastal areas which had been fished and managed by consecutive generations of Māori; kina, Evechinus chloroticus, sea urchin; koura, Jasus edwardsii, red rock lobster; kūtai, Perna canaliculus, green lipped mussel; and pāua, Haliotis iris, abalone. This knowledge was then mapped and used as the baseline for sub-tidal marine science field research surveys. Findings from the transdisciplinary marine research was used to develop management actions to assist Māori and Government entities for improving, enhancing and safeguarding marine taonga species into the future. This article critically discusses and demonstrates the relevance and complementarity of mātauranga Māori and Western science, and the importance of kaupapa Māori strategies for empowering Māori collaboration and voices in marine research co-development, implementation and communication.

year: 2020